From 9ee3515035bd5039d7572dc736635f689c2d1131 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Sun, 12 Jan 2025 14:25:01 +0000 Subject: [PATCH] Spelling fixes Gbp-Pq: Name spelling --- c++/include/objtools/alnmgr/seqids_extractor.hpp | 2 +- c++/src/algo/winmask/seq_masker_ostat_factory.cpp | 4 ++-- c++/src/app/blastdb/blastdbcheck.cpp | 2 +- c++/src/app/blastdb/makeprofiledb.cpp | 2 +- c++/src/objects/seqalign/Dense_seg.cpp | 2 +- c++/src/objects/seqalign/Seq_align.cpp | 2 +- c++/src/objects/seqfeat/institution_codes.inc | 2 +- c++/src/objects/seqfeat/institution_codes.txt | 2 +- c++/src/objmgr/util/sequence.cpp | 2 +- c++/src/objtools/align_format/taxFormat.cpp | 2 +- c++/src/objtools/format/flat_file_config.cpp | 2 +- c++/src/objtools/readers/agp_converter.cpp | 2 +- c++/src/objtools/readers/agp_util.cpp | 4 ++-- c++/src/objtools/readers/agp_validate_reader.cpp | 2 +- c++/src/util/compress/api/compress.cpp | 2 +- 15 files changed, 17 insertions(+), 17 deletions(-) diff --git a/c++/include/objtools/alnmgr/seqids_extractor.hpp b/c++/include/objtools/alnmgr/seqids_extractor.hpp index d38e3769..359f02ef 100644 --- a/c++/include/objtools/alnmgr/seqids_extractor.hpp +++ b/c++/include/objtools/alnmgr/seqids_extractor.hpp @@ -232,7 +232,7 @@ public: else if (*id_vec[i] != *id) { string err("Inconsistent Seq-ids found in seg "); err += NStr::NumericToString(i) + - ". Excpected " + id_vec[i]->AsString() + + ". Expected " + id_vec[i]->AsString() + ", encountered " + id->AsString() + "."; NCBI_THROW(CAlnException, eInvalidSeqId, err); } diff --git a/c++/src/algo/winmask/seq_masker_ostat_factory.cpp b/c++/src/algo/winmask/seq_masker_ostat_factory.cpp index 74263c51..eeaba1a0 100644 --- a/c++/src/algo/winmask/seq_masker_ostat_factory.cpp +++ b/c++/src/algo/winmask/seq_masker_ostat_factory.cpp @@ -75,7 +75,7 @@ CSeqMaskerOstat * CSeqMaskerOstatFactory::create( } else NCBI_THROW( CSeqMaskerOstatFactoryException, eBadName, - "unkown unit counts format" ); + "unknown unit counts format" ); } catch( CException & e ) { NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail, @@ -113,7 +113,7 @@ CSeqMaskerOstat * CSeqMaskerOstatFactory::create( } else NCBI_THROW( CSeqMaskerOstatFactoryException, eBadName, - "unkown unit counts format" ); + "unknown unit counts format" ); } catch( CException & e ) { NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail, diff --git a/c++/src/app/blastdb/blastdbcheck.cpp b/c++/src/app/blastdb/blastdbcheck.cpp index 8084fec5..94841764 100644 --- a/c++/src/app/blastdb/blastdbcheck.cpp +++ b/c++/src/app/blastdb/blastdbcheck.cpp @@ -245,7 +245,7 @@ void CBlastDbCheckApplication::Init(void) "Require that all sequences in the database have taxid set."); arg_desc->AddFlag - ("cdd_delta", "Do aditional tests for a CDD database for DELTA-BLAST"); + ("cdd_delta", "Do additional tests for a CDD database for DELTA-BLAST"); // Setup arg.descriptions for this application SetupArgDescriptions(arg_desc.release()); diff --git a/c++/src/app/blastdb/makeprofiledb.cpp b/c++/src/app/blastdb/makeprofiledb.cpp index 1135fe06..77692af5 100644 --- a/c++/src/app/blastdb/makeprofiledb.cpp +++ b/c++/src/app/blastdb/makeprofiledb.cpp @@ -1838,7 +1838,7 @@ bool CMakeProfileDBApp::x_CheckDelta( const CPssm & pssm, Int4 seq_size, const if( !x_ValidateCd(freqs, obsr, BLASTAA_SIZE) && m_ExcludeInvalid) { *m_LogFile << filename + - " was excluded: it conatins an invalid CD \n"; + " was excluded: it contains an invalid CD \n"; return false; } return true; diff --git a/c++/src/objects/seqalign/Dense_seg.cpp b/c++/src/objects/seqalign/Dense_seg.cpp index 015614ca..85f396f1 100644 --- a/c++/src/objects/seqalign/Dense_seg.cpp +++ b/c++/src/objects/seqalign/Dense_seg.cpp @@ -980,7 +980,7 @@ void CDense_seg::RemapToLoc(TDim row, const CSeq_loc& loc, if (loc_plus != (seq_loc_i.GetStrand() != eNa_strand_minus)) { NCBI_THROW(CSeqalignException, eInvalidInputData, "CDense_seg::RemapToLoc():" - " The strand should be the same accross" + " The strand should be the same across" " the input seq-loc"); } } diff --git a/c++/src/objects/seqalign/Seq_align.cpp b/c++/src/objects/seqalign/Seq_align.cpp index 3ceefedc..eb27ce2c 100644 --- a/c++/src/objects/seqalign/Seq_align.cpp +++ b/c++/src/objects/seqalign/Seq_align.cpp @@ -872,7 +872,7 @@ CSeq_align::CreateDensegFromStdseg(SSeqIdChooser* SeqIdChooser) const if (dim != ss.GetDim() || row != dim) { NCBI_THROW(CSeqalignException, eInvalidInputAlignment, "CreateDensegFromStdseg(): " - "Inconsistent dimentions!"); + "Inconsistent dimensions!"); } if (widths_determined[seg]) { diff --git a/c++/src/objects/seqfeat/institution_codes.inc b/c++/src/objects/seqfeat/institution_codes.inc index b11f9cce..79511521 100644 --- a/c++/src/objects/seqfeat/institution_codes.inc +++ b/c++/src/objects/seqfeat/institution_codes.inc @@ -791,7 +791,7 @@ static const char* const kInstitutionCollectionCodeList[] = { "BPPT-ESC\tc\tBPPT Ethanol-Single Cell Protein-Fructose Syrup Technical Unit\t\t\t", "BPU\ts\tEoetvoes Lorand University, Department of Plant Taxonomy and Ecology\t\t\t", "BR\ts\tBotanic Garden Meise\t\t\t", -"BR\tc\tJohanna Dobereiner Biological Resouce Center (CRB-JD)\t\t\t", +"BR\tc\tJohanna Dobereiner Biological Resource Center (CRB-JD)\t\t\t", "BRA\ts\tSlovak National Museum, Botany Department\t\t\t", "BRAD\ts\tUniversity of Bradford, Biology Department\t\t\t", "BRB\ts\tBrassica Resource Bank\t\t\t", diff --git a/c++/src/objects/seqfeat/institution_codes.txt b/c++/src/objects/seqfeat/institution_codes.txt index 4ba3f544..8848d3d0 100644 --- a/c++/src/objects/seqfeat/institution_codes.txt +++ b/c++/src/objects/seqfeat/institution_codes.txt @@ -755,7 +755,7 @@ BPM s Beipiao Paleontological Museum BPPT-ESC c BPPT Ethanol-Single Cell Protein-Fructose Syrup Technical Unit BPU s Eoetvoes Lorand University, Department of Plant Taxonomy and Ecology BR s Botanic Garden Meise -BR c Johanna Dobereiner Biological Resouce Center (CRB-JD) +BR c Johanna Dobereiner Biological Resource Center (CRB-JD) BRA s Slovak National Museum, Botany Department BRAD s University of Bradford, Biology Department BRB s Brassica Resource Bank diff --git a/c++/src/objmgr/util/sequence.cpp b/c++/src/objmgr/util/sequence.cpp index 7896fcb2..07913b1f 100644 --- a/c++/src/objmgr/util/sequence.cpp +++ b/c++/src/objmgr/util/sequence.cpp @@ -385,7 +385,7 @@ string GetProteinName(const CBioseq_Handle& seq) if ( best_feats.empty() ) { NCBI_THROW_FMT(CObjMgrException, eFindFailed, "GetProteinName("< 1 ) { NCBI_THROW_FMT(CObjMgrException, eFindConflict, diff --git a/c++/src/objtools/align_format/taxFormat.cpp b/c++/src/objtools/align_format/taxFormat.cpp index 49b95ad2..4307302b 100644 --- a/c++/src/objtools/align_format/taxFormat.cpp +++ b/c++/src/objtools/align_format/taxFormat.cpp @@ -616,7 +616,7 @@ void CTaxFormat::x_LoadTaxTree(void) } } if (!tax_load_ok) { - NCBI_THROW(CException, eUnknown,"Taxonomic load was not successfull."); + NCBI_THROW(CException, eUnknown,"Taxonomic load was not successful."); } m_TaxTreeLoaded = true; diff --git a/c++/src/objtools/format/flat_file_config.cpp b/c++/src/objtools/format/flat_file_config.cpp index ae006f92..75445dc5 100644 --- a/c++/src/objtools/format/flat_file_config.cpp +++ b/c++/src/objtools/format/flat_file_config.cpp @@ -655,7 +655,7 @@ void CFlatFileConfig::AddArgumentDescriptions(CArgDescriptions& args) // from arg_desc->AddOptionalKey("from", "From", - "Begining of shown range", CArgDescriptions::eInteger); + "Beginning of shown range", CArgDescriptions::eInteger); // to arg_desc->AddOptionalKey("to", "To", diff --git a/c++/src/objtools/readers/agp_converter.cpp b/c++/src/objtools/readers/agp_converter.cpp index 20084f30..ce844abd 100644 --- a/c++/src/objtools/readers/agp_converter.cpp +++ b/c++/src/objtools/readers/agp_converter.cpp @@ -728,7 +728,7 @@ void CAgpConverter::x_SetUpObjectOpeningAndClosingStrings( submit_block_writer.WriteObject(m_pSubmitBlock.GetPointer(), m_pSubmitBlock->GetThisTypeInfo()); submit_block_writer.Flush(); seq_sub_header_strm << "," << endl; - seq_sub_header_strm << "data entrys {" << endl; + seq_sub_header_strm << "data entries {" << endl; out_sObjectOpeningString = seq_sub_header_strm.str(); out_sObjectClosingString = "} }" + out_sObjectClosingString; diff --git a/c++/src/objtools/readers/agp_util.cpp b/c++/src/objtools/readers/agp_util.cpp index 4284710c..bfd5b892 100644 --- a/c++/src/objtools/readers/agp_util.cpp +++ b/c++/src/objtools/readers/agp_util.cpp @@ -173,7 +173,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= { "object_beg != previous object_end + 1", "no valid AGP lines", - "consequtive gaps lines with the same type and linkage", + "consecutive gaps lines with the same type and linkage", "in \"Scaffold from component\" file, invalid scaffold-breaking gap", "in \"Chromosome from scaffold\" file, invalid \"within-scaffold\" gap", @@ -193,7 +193,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= { // Content Warnings "gap at the end of object (OK if X is the circular chromosome/plasmid)", "gap at the beginning of object ", - "two consequtive gap lines (e.g. a gap at the end of " + "two consecutive gap lines (e.g. a gap at the end of " "a scaffold, two non scaffold-breaking gaps, ...)", "no components in object", "the span overlaps a previous span for this component", diff --git a/c++/src/objtools/readers/agp_validate_reader.cpp b/c++/src/objtools/readers/agp_validate_reader.cpp index b15a7663..7977c7b3 100644 --- a/c++/src/objtools/readers/agp_validate_reader.cpp +++ b/c++/src/objtools/readers/agp_validate_reader.cpp @@ -300,7 +300,7 @@ void CAgpValidateReader::OnGapOrComponent() int prev_comp_file=spans.rbegin()->file_num; int prev_comp_line=spans.rbegin()->line_num; if(prev_comp_file < m_last_scaf_start_file || prev_comp_line < m_last_scaf_start_line) { - sameComId_otherScaf="; previous occurance at "; + sameComId_otherScaf="; previous occurrence at "; if(prev_comp_file && prev_comp_file!=m_AgpErr->GetFileNum()) { sameComId_otherScaf += m_AgpErr->GetFile(prev_comp_file); sameComId_otherScaf += ":"; diff --git a/c++/src/util/compress/api/compress.cpp b/c++/src/util/compress/api/compress.cpp index 5da4619e..6a1817ae 100644 --- a/c++/src/util/compress/api/compress.cpp +++ b/c++/src/util/compress/api/compress.cpp @@ -165,7 +165,7 @@ bool CCompression::x_DecompressFile(CCompressionFile& src_file, while ( (nread = src_file.Read(buf.get(), file_io_bufsize)) > 0 ) { os.write(buf.get(), nread); if ( !os.good() ) { - SetError(-1, "Error writing to ouput file"); + SetError(-1, "Error writing to output file"); return false; } } -- 2.30.2